Substrate-based chemical probes for Alzheimer’s γ-secretase

Abstract

The membrane-embedded γ-secretase complex carries out hydrolysis within the lipid bilayer in proteolyzing nearly 100 different membrane protein substrates. Among these substrates, the amyloid precursor protein (APP) has been the most studied, as generation of aggregation-prone amyloid β-peptide (Aβ) is a defining feature of Alzheimer’s disease (AD). Mutations in APP and in presenilin, the catalytic component of γ-secretase, cause familial AD, strong evidence for a pathogenic role of Aβ. However, in human trials γ-secretase inhibitors not only failed to slow AD progression, they worsened cognitive function. More in-depth study of γ-secretase and how AD-causing mutations alter its structure and function is clearly needed. Substrate-based chemical probes have been critical to unraveling the complexity of γ-secretase. Such synthetic peptides and peptidomimetics will be reviewed here, including recently reported structural and functional probes.

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Abbreviations

Alzheimer’s disease:

AD

α-aminoisobutyric acid:

Aib

Amyloid β-peptide:

Amyloid precursor protein:

APP

Amyloid precursor protein intracellular domain:

AICD

99-residue APP membrane-bound stub:

C99

C-terminal fragment:

CTF

Familial Alzheimer’s disease:

FAD

Cryo-electron microscopy:

cryo-EM

Helical peptide inhibitor:

HPI

N-terminal fragment:

NTF

Presenilin-1:

PSEN1

Presenilin-2:

PSEN2

Transition-state analog inhibitor:

TSA

Transmembrane domain:

TMD

References

  1. Bai XC, Rajendra E, Yang G, Shi Y, Scheres SH (2015) Sampling the conformational space of the catalytic subunit of human γ-secretase. eLife 4:pii: e11182

    Google Scholar 

  2. Beel AJ, Sanders CR (2008) Substrate specificity of γ-secretase and other intramembrane proteases. Cell Mol Life Sci 65:1311–1334

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Bhattarai S, Devkota S, Meneely KM, Xing M, Douglas JT, Wolfe MS (2020) Design of Substrate Transmembrane Mimetics as Structural Probes for γ-Secretase. J Am Chem Soc 142:3351–3355

    CAS  PubMed  Google Scholar 

  4. Bihel F, Das C, Bowman MJ, Wolfe MS (2004) Discovery of a subnanomolar helical D-tridecapeptide inhibitor of γ-secretase. J Med Chem 47:3931–3933

    CAS  PubMed  Google Scholar 

  5. Bolduc DM, Montagna DR, Gu Y, Selkoe DJ, Wolfe MS (2016a) Nicastrin functions to sterically hinder γ-secretase-substrate interactions driven by substrate transmembrane domain. Proc Natl Acad Sci USA 113:E509–518

    CAS  PubMed  Google Scholar 

  6. Bolduc DM, Montagna DR, Seghers MC, Wolfe MS, Selkoe DJ (2016b) The amyloid-β forming tripeptide cleavage mechanism of γ-secretase. eLife 5:pii: e17578

    Google Scholar 

  7. Borchelt DR, Thinakaran G, Eckman CB, Lee MK, Davenport F, Ratovitsky T, Prada CM, Kim G, Seekins S, Yager D, Slunt HH, Wang R, Seeger M, Levey AI, Gandy SE, Copeland NG, Jenkins NA, Price DL, Younkin SG, Sisodia SS (1996) Familial Alzheimer’s disease-linked presenilin 1 variants elevate Aβ1-42/1-40 ratio in vitro and in vivo. Neuron 17:1005–1013

    CAS  PubMed  Google Scholar 

  8. Chartier-Harlin MC, Crawford F, Houlden H, Warren A, Hughes D, Fidani L, Goate A, Rossor M, Roques P, Hardy J et al. (1991) Early-onset Alzheimer’s disease caused by mutations at codon 717 of the β-amyloid precursor protein gene. Nature 353:844–846

    CAS  PubMed  Google Scholar 

  9. Citron M, Westaway D, Xia W, Carlson G, Diehl T, Levesque G, Johnson-Wood K, Lee M, Seubert P, Davis A, Kholodenko D, Motter R, Sherrington R, Perry B, Yao H, Strome R, Lieberburg I, Rommens J, Kim S, Schenk D, Fraser P, St George Hyslop P, Selkoe DJ (1997) Mutant presenilins of Alzheimer’s disease increase production of 42-residue amyloid β-protein in both transfected cells and transgenic mice. Nat Med 3:67–72

    CAS  PubMed  Google Scholar 

  10. Cole SL, Vassar R (2008) The role of APP processing by BACE1, the β-secretase, in Alzheimer’s disease pathophysiology. J Biol Chem 283:29621–29625

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Coric V, Salloway S, van Dyck CH, Dubois B, Andreasen N, Brody M, Curtis C, Soininen H, Thein S, Shiovitz T, Pilcher G, Ferris S, Colby S, Kerselaers W, Dockens R, Soares H, Kaplita S, Luo F, Pachai C, Bracoud L, Mintun M, Grill JD, Marek K, Seibyl J, Cedarbaum JM, Albright C, Feldman HH, Berman RM (2015) Targeting prodromal Alzheimer disease with avagacestat: a randomized clinical trial. JAMA Neurol 72:1324–1333

    PubMed  Google Scholar 

  12. Das C, Berezovska O, Diehl TS, Genet C, Buldyrev I, Tsai JY, Hyman BT, Wolfe MS (2003) Designed helical peptides inhibit an intramembrane protease. J Am Chem Soc 125:11794–11795

    CAS  PubMed  Google Scholar 

  13. De Strooper B, Saftig P, Craessaerts K, Vanderstichele H, Guhde G, Annaert W, Von Figura K, Van Leuven F (1998) Deficiency of presenilin-1 inhibits the normal cleavage of amyloid precursor protein. Nature 391:387–390

    PubMed  Google Scholar 

  14. Doody RS, Raman R, Farlow M, Iwatsubo T, Vellas B, Joffe S, Kieburtz K, He F, Sun X, Thomas RG, Aisen PS, Siemers E, Sethuraman G, Mohs R (2013) A phase 3 trial of semagacestat for treatment of Alzheimer’s disease. N Eng J Med 369:341–350

    CAS  Google Scholar 

  15. Duff K, Eckman C, Zehr C, Yu X, Prada CM, Perez-tur J, Hutton M, Buee L, Harigaya Y, Yager D, Morgan D, Gordon MN, Holcomb L, Refolo L, Zenk B, Hardy J, Younkin S (1996) Increased amyloid-β42(43) in brains of mice expressing mutant presenilin 1. Nature 383:710–713

    CAS  PubMed  Google Scholar 

  16. Edbauer D, Winkler E, Regula JT, Pesold B, Steiner H, Haass C (2003) Reconstitution of γ-secretase activity. Nat Cell Biol 5:486–488

    CAS  PubMed  Google Scholar 

  17. Esler WP, Das C, Wolfe MS (2004) Probing pockets S2-S4’ of the γ-secretase active site with (hydroxyethyl)urea peptidomimetics. Bioorg Med Chem Lett 14:1935–1938

    CAS  PubMed  Google Scholar 

  18. Esler WP, Kimberly WT, Ostaszewski BL, Diehl TS, Moore CL, Tsai J-Y, Rahmati T, Xia W, Selkoe DJ, Wolfe MS (2000) Transition-state analogue inhibitors of γ-secretase bind directly to presenilin-1. Nat Cell Biol 2:428–434

    CAS  PubMed  Google Scholar 

  19. Esler WP, Kimberly WT, Ostaszewski BL, Ye W, Diehl TS, Selkoe DJ, Wolfe MS (2002) Activity-dependent isolation of the presenilin/γ-secretase complex reveals nicastrin and a γ substrate. Proc Natl Acad Sci USA 99:2720–2725

    CAS  PubMed  Google Scholar 

  20. Fernandez MA, Klutkowski JA, Freret T, Wolfe MS (2014) Alzheimer presenilin-1 mutations dramatically reduce trimming of long amyloid β-peptides (Aβ) by γ-secretase to increase 42-to-40-residue Aβ. J Biol Chem 289:31043–31052

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Fraering PC, LaVoie MJ, Ye W, Ostaszewski BL, Kimberly WT, Selkoe DJ, Wolfe MS (2004a) Detergent-dependent dissociation of active γ-secretase reveals an interaction between Pen-2 and PS1-NTF and offers a model for subunit organization within the complex. Biochemistry 43:323–333

    CAS  PubMed  Google Scholar 

  22. Fraering PC, Ye W, Strub JM, Dolios G, LaVoie MJ, Ostaszewski BL, Van Dorsselaer A, Wang R, Selkoe DJ, Wolfe MS (2004b) Purification and Characterization of the Human γ-Secretase Complex. Biochemistry 43:9774–9789

    CAS  PubMed  Google Scholar 

  23. Francis R, McGrath G, Zhang J, Ruddy DA, Sym M, Apfeld J, Nicoll M, Maxwell M, Hai B, Ellis MC, Parks AL, Xu W, Li J, Gurney M, Myers RL, Himes CS, Hiebsch R, Ruble C, Nye JS, Curtis D (2002) aph-1 and pen-2 are required for Notch pathway signaling, γ-secretase cleavage of βAPP, and presenilin protein accumulation. Dev Cell 3:85–97

    CAS  PubMed  Google Scholar 

  24. Goate A, Chartier-Harlin MC, Mullan M, Brown J, Crawford F, Fidani L, Giuffra L, Haynes A, Irving N, James L et al. (1991) Segregation of a missense mutation in the amyloid precursor protein gene with familial Alzheimer’s disease. Nature 349:704–706

    CAS  PubMed  Google Scholar 

  25. Goutte C, Tsunozaki M, Hale VA, Priess JR (2002) APH-1 is a multipass membrane protein essential for the Notch signaling pathway in Caenorhabditis elegans embryos. Proc Natl Acad Sci USA 99:775–779

    CAS  PubMed  Google Scholar 

  26. Gu Y, Misonou H, Sato T, Dohmae N, Takio K, Ihara Y (2001) Distinct intramembrane cleavage of the β-amyloid precursor protein family resembling γ-secretase-like cleavage of Notch. J Biol Chem 276:35235–35238

    CAS  PubMed  Google Scholar 

  27. Hardy J, Allsop D (1991) Amyloid deposition as the central event in the aetiology of Alzheimer’s disease. Trends Pharm Sci 12:383–388

    CAS  PubMed  Google Scholar 

  28. Hemming ML, Elias JE, Gygi SP, Selkoe DJ (2008) Proteomic profiling of γ-secretase substrates and mapping of substrate requirements. PLoS Biol 6:e257

    PubMed  PubMed Central  Google Scholar 

  29. Herreman A, Serneels L, Annaert W, Collen D, Schoonjans L, De Strooper B (2000) Total inactivation of γ-secretase activity in presenilin-deficient embryonic stem cells. Nat Cell Biol 2:461–462

    CAS  PubMed  Google Scholar 

  30. Kimberly WT, LaVoie MJ, Ostaszewski BL, Ye W, Wolfe MS, Selkoe DJ (2003) γ-Secretase is a membrane protein complex comprised of presenilin, nicastrin, aph-1, and pen-2. Proc Natl Acad Sci USA 100:6382–6387

    CAS  PubMed  Google Scholar 

  31. Kopan R, Ilagan MX (2004) γ-Secretase: proteasome of the membrane? Nat Rev Mol Cell Biol 5:499–504

    CAS  PubMed  Google Scholar 

  32. Kornilova AY, Bihel F, Das C, Wolfe MS (2005) The initial substrate-binding site of γ-secretase is located on presenilin near the active site. Proc Natl Acad Sci USA 102:3230–3235

    CAS  PubMed  Google Scholar 

  33. Li X, Dang S, Yan C, Gong X, Wang J, Shi Y (2013) Structure of a presenilin family intramembrane aspartate protease. Nature 493:56–61

    PubMed  Google Scholar 

  34. Li YM, Xu M, Lai MT, Huang Q, Castro JL, DiMuzio-Mower J, Harrison T, Lellis C, Nadin A, Neduvelil JG, Register RB, Sardana MK, Shearman MS, Smith AL, Shi XP, Yin KC, Shafer JA, Gardell SJ (2000) Photoactivated γ-secretase inhibitors directed to the active site covalently label presenilin 1. Nature 405:689–694

    CAS  PubMed  Google Scholar 

  35. Lu P, Bai XC, Ma D, Xie T, Yan C, Sun L, Yang G, Zhao Y, Zhou R, Scheres SH, Shi Y (2014) Three-dimensional structure of human γ-secretase. Nature 512:166–170

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Moore CL, Leatherwood DD, Diehl TS, Selkoe DJ, Wolfe MS (2000) Difluoro ketone peptidomimetics suggest a large S1 pocket for Alzheimer’s γ-secretase: implications for inhibitor design. J Med Chem 43:3434–3442

    CAS  PubMed  Google Scholar 

  37. Philip AT, Devkota S, Malvankar S, Bhattarai S, Meneely KM, Williams TD, Wolfe MS (2019) Designed helical peptides as functional probes for γ-secretase. Biochemistry 58:4398–4407

    CAS  PubMed  Google Scholar 

  38. Qi-Takahara Y, Morishima-Kawashima M, Tanimura Y, Dolios G, Hirotani N, Horikoshi Y, Kametani F, Maeda M, Saido TC, Wang R, Ihara Y (2005) Longer forms of amyloid β protein: implications for the mechanism of intramembrane cleavage by γ-secretase. J Neurosci 25:436–445

    CAS  PubMed  PubMed Central  Google Scholar 

  39. Querfurth HW, LaFerla FM (2010) Alzheimer’s disease. N Eng J Med 362:329–344

    CAS  Google Scholar 

  40. Rogaev EI, Sherrington R, Rogaeva EA, Levesque G, Ikeda M, Liang Y, Chi H, Lin C, Holman K, Tsuda T, Mar L, Sorbi S, Nacmias B, Placentini S, Amaducci L, Chumakov I, Cohen D, Lannfelt L, Fraser PE, Rommens JM, St George Hyslop PH (1995) Familial Alzheimer’s disease in kindreds with missense mutations in a gene on chromosome 1 related to the Alzheimer’s disease type 3 gene. Nature 376:775–778

    CAS  PubMed  Google Scholar 

  41. Sastre M, Steiner H, Fuchs K, Capell A, Multhaup G, Condron MM, Teplow DB, Haass C (2001) Presenilin-dependent γ-secretase processing of β-amyloid precursor protein at a site corresponding to the S3 cleavage of Notch. EMBO Rep. 2:835–841

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Sato T, Dohmae N, Qi Y, Kakuda N, Misonou H, Mitsumori R, Maruyama H, Koo EH, Haass C, Takio K, Morishima-Kawashima M, Ishiura S, Ihara Y (2003) Potential link between amyloid β-protein 42 and C-terminal fragment γ49-99 of β-amyloid precursor protein. J Biol Chem 278:24294–24301

    CAS  PubMed  Google Scholar 

  43. Scheuner D, Eckman C, Jensen M, Song X, Citron M, Suzuki N, Bird TD, Hardy J, Hutton M, Kukull W, Larson E, Levy-Lahad E, Viitanen M, Peskind E, Poorkaj P, Schellenberg G, Tanzi R, Wasco W, Lannfelt L, Selkoe D, Younkin S (1996) Secreted amyloid β-protein similar to that in the senile plaques of Alzheimer’s disease is increased in vivo by the presenilin 1 and 2 and APP mutations linked to familial Alzheimer’s disease. Nat Med 2:864–870

    CAS  PubMed  Google Scholar 

  44. Selkoe DJ (1991) The molecular pathology of Alzheimer’s disease. Neuron 6:487–498

    CAS  PubMed  Google Scholar 

  45. Shearman MS, Beher D, Clarke EE, Lewis HD, Harrison T, Hunt P, Nadin A, Smith AL, Stevenson G, Castro JL (2000) L-685,458, an aspartyl protease transition state mimic, is a potent inhibitor of amyloid β-protein precursor γ-secretase activity. Biochemistry 39:8698–8704

    CAS  PubMed  Google Scholar 

  46. Sherrington R, Rogaev EI, Liang Y, Rogaeva EA, Levesque G, Ikeda M, Chi H, Lin C, Li G, Holman K, Tsuda T, Mar L, Foncin JF, Bruni AC, Montesi MP, Sorbi S, Rainero I, Pinessi L, Nee L, Chumakov I, Pollen D, Brookes A, Sanseau P, Polinsky RJ, Wasco W, Da Silva HA, Haines JL, Perkicak-Vance MA, Tanzi RE, Roses AD, Fraser PE, Rommens JM, St George-Hyslop PH (1995) Cloning of a gene bearing missense mutations in early-onset familial Alzheimer’s disease. Nature 375:754–760

    CAS  PubMed  Google Scholar 

  47. Steiner H, Winkler E, Haass C (2008) Chemical crosslinking provides a model of the γ-secretase complex subunit architecture and evidence for close proximity of the C-terminal fragment of presenilin with APH-1. J Biol Chem 283:34677–34686

    CAS  PubMed  PubMed Central  Google Scholar 

  48. Takami M, Nagashima Y, Sano Y, Ishihara S, Morishima-Kawashima M, Funamoto S, Ihara Y (2009) γ-Secretase: successive tripeptide and tetrapeptide release from the transmembrane domain of beta-carboxyl terminal fragment. J Neurosci 29:13042–13052

    CAS  PubMed  PubMed Central  Google Scholar 

  49. Takasugi N, Tomita T, Hayashi I, Tsuruoka M, Niimura M, Takahashi Y, Thinakaran G, Iwatsubo T (2003) The role of presenilin cofactors in the γ-secretase complex. Nature 422:438–441

    CAS  PubMed  Google Scholar 

  50. Tanzi RE, Bertram L (2005) Twenty years of the Alzheimer’s disease amyloid hypothesis: a genetic perspective. Cell 120:545–555

    CAS  PubMed  Google Scholar 

  51. Weidemann A, Eggert S, Reinhard FB, Vogel M, Paliga K, Baier G, Masters CL, Beyreuther K, Evin G (2002) A novel var epsilon-cleavage within the transmembrane domain of the Alzheimer amyloid precursor protein demonstrates homology with Notch processing. Biochemistry 41:2825–2835

    CAS  PubMed  Google Scholar 

  52. Wolfe MS (2019) Structure and function of the γ-secretase complex. Biochemistry 58:2953–2966

    CAS  PubMed  PubMed Central  Google Scholar 

  53. Wolfe MS, Citron M, Diehl TS, Xia W, Donkor IO, Selkoe DJ (1998) A substrate-based difluoro ketone selectively inhibits Alzheimer’s γ-secretase activity. J medicinal Chem 41:6–9

    CAS  Google Scholar 

  54. Wolfe MS, Xia W, Moore CL, Leatherwood DD, Ostaszewski B, Donkor IO, Selkoe DJ (1999a) Peptidomimetic probes and molecular modeling suggest Alzheimer’s γ-secretases are intramembrane-cleaving aspartyl proteases. Biochemistry 38:4720–4727

    CAS  PubMed  Google Scholar 

  55. Wolfe MS, Xia W, Ostaszewski BL, Diehl TS, Kimberly WT, Selkoe DJ (1999b) Two transmembrane aspartates in presenilin-1 required for presenilin endoproteolysis and γ-secretase activity. Nature 398:513–517

    CAS  PubMed  Google Scholar 

  56. Yagishita S, Morishima-Kawashima M, Ishiura S, Ihara Y (2008) Aβ46 is processed to Aβ40 and Aβ43, but not to Aβ42, in the low density membrane domains. J Biol Chem 283:733–738

    CAS  PubMed  Google Scholar 

  57. Yang G, Zhou R, Zhou Q, Guo X, Yan C, Ke M, Lei J, Shi Y (2019) Structural basis of notch recognition by human γ-secretase. Nature 565:192–197

    CAS  PubMed  Google Scholar 

  58. Yu C, Kim SH, Ikeuchi T, Xu H, Gasparini L, Wang R, Sisodia SS (2001) Characterization of a presenilin-mediated amyloid precursor protein carboxyl-terminal fragment γ. Evidence for distinct mechanisms involved in γ-secretase processing of the APP and Notch1 transmembrane domains. J Biol Chem 276:43756–43760

    CAS  PubMed  Google Scholar 

  59. Yu G, Nishimura M, Arawaka S, Levitan D, Zhang L, Tandon A, Song YQ, Rogaeva E, Chen F, Kawarai T, Supala A, Levesque L, Yu H, Yang DS, Holmes E, Milman P, Liang Y, Zhang DM, Xu DH, Sato C, Rogaev E, Smith M, Janus C, Zhang Y, Aebersold R, Farrer LS, Sorbi S, Bruni A, Fraser P, St George-Hyslop P (2000) Nicastrin modulates presenilin-mediated notch/glp-1 signal transduction and βAPP processing. Nature 407:48–54

    CAS  PubMed  Google Scholar 

  60. Zhang Z, Nadeau P, Song W, Donoviel D, Yuan M, Bernstein A, Yankner BA (2000) Presenilins are required for γ-secretase cleavage of β-APP and transmembrane cleavage of Notch-1. Nat Cell Biol 2:463–465

    CAS  PubMed  Google Scholar 

  61. Zhao G, Cui MZ, Mao G, Dong Y, Tan J, Sun L, Xu X (2005) γ-Cleavage is dependent on ζ-cleavage during the proteolytic processing of amyloid precursor protein within its transmembrane domain. J Biol Chem 280:37689–37697

    CAS  PubMed  Google Scholar 

  62. Zhou R, Yang G, Guo X, Zhou Q, Lei J, Shi Y (2019) Recognition of the amyloid precursor protein by human γ-secretase. Science 363:eaaw0930

    CAS  PubMed  Google Scholar 

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Acknowledgements

This work was supported by grant GM122894 from the NIH.

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Correspondence to Michael S. Wolfe.

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Wolfe, M.S. Substrate-based chemical probes for Alzheimer’s γ-secretase. Med Chem Res 29, 1122–1132 (2020). https://doi.org/10.1007/s00044-020-02565-w

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Keywords

  • Protease
  • Inhibitors
  • Amyloid
  • Alzheimer’s disease